PT  - JOURNAL ARTICLE
AU  - Krasheninina, Olga
AU  - Hwang, Yih-Chii
AU  - Bai, Xiaodong
AU  - Zalcman, Aleksandra
AU  - Maxwell, Evan
AU  - Reid, Jeffrey G.
AU  - Salerno, William J.
TI  - Open-source mapping and variant calling for large-scale NGS data from original base-quality scores
AID  - 10.1101/2020.12.15.356360
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.12.15.356360
4099  - http://biorxiv.org/content/early/2020/12/16/2020.12.15.356360.short
4100  - http://biorxiv.org/content/early/2020/12/16/2020.12.15.356360.full
AB  - Standardized genome informatics protocols minimize reprocessing costs and facilitate harmonization across studies if implemented in a transparent, accessible and reproducible manner. Here we define the OQFE protocol, a lossless read-mapping protocol that retains key features of existing NGS standard methods. We demonstrate that variants can be called directly from NovaSeq OQFE data without the need for base quality score recalibration and describe a large-scale variant calling protocol for OQFE data. The OQFE protocol is open-source and a containerized implementation is provided.Competing Interest StatementThe authors have declared no competing interest.